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  • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G01N33/57407—Specifically defined cancers
  • G01N33/57438—Specifically defined cancers of liver, pancreas or kidney
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  • A61P1/18—Drugs for disorders of the alimentary tract or the digestive system for pancreatic disorders, e.g. pancreatic enzymes
• • A—HUMAN NECESSITIES
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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
  • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • C12Q2600/00—Oligonucleotides characterized by their use
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• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
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Definitions

• the invention relates to methods of diagnosing pancreatic cancer.
• Pancreatic cancer has one of the highest mortality rates of any malignancy, and the 5- year-survival rate of patients is 4%. 28000 patients with pancreatic cancer are diagnosed each year, and nearly all patients will die of their disease (1). The poor prognosis of this malignancy is a result of the difficulty of early diagnosis and poor response to current therapeutic methods (1, 2). In particular currently no tumor markers are identified that allow reliable screening at an early, potentially curative stage of the disease.
• cDNA microarray technologies have enabled to obtain comprehensive profiles of gene expression in normal and malignant cells, and compare the gene expression in malignant and corresponding normal cells (Okabe et al., Cancer Res 61:2129-37 (2001); Kitahara et al., Cancer Res 61: 3544-9 (2001); Lin et al, Oncogene 21:4120-8 (2002); Hasegawa et al, Cancer Res 62:7012-7 (2002)).
• This approach enables to disclose the complex nature of cancer cells, and helps to understand the mechanism of carcinogenesis. Identification of genes that are deregulated in tumors can lead to more precise and accurate diagnosis of individual cancers, and to develop novel therapeutic targets (Bienz and Clevers, Cell 103:311- 20 (2000)).
• FTIs farnexyltransferase
• trastuzumab Clinical trials on human using a combination or anti-cancer drugs and anti-HER2 monoclonal antibody, trastuzumab, have been conducted to antagonize the proto-oncogene receptor HER2/ neu; and have been achieving improved clinical response and overall survival of breast-cancer patients (Lin et al., Cancer Res 61:6345-9 (2001)).
• a tyrosine kinase inhibitor, STI-571 which selectively inactivates bcr-abl fusion proteins, has been developed to treat chronic myelogenous leukemias wherein constitutive activation of bcr-abl tyrosine kinase plays a crucial role in the transformation of leukocytes.
• Agents of these kinds are designed to suppress oncogenic activity of specific gene products (Fujita et al, Cancer Res 61 -.1122-6 (2001)). Therefore, gene products commonly up-regulated in cancerous cells may serve as potential targets for developing novel anti-cancer agents.
• CTLs cytotoxic T lymphocytes
• TAAs tumor-associated antigens
• TAAs are now in the stage of clinical development as targets of immunotherapy. TAAs discovered so far include MAGE (van der Bruggen et al, Science 254: 1643-7 (1991)), gplOO (Kawakami et al, J Exp Med 180: 347-52 (1994)), SART (Shichijo et al., J Exp Med 187: 277-88 (1998)), and NY-ESO-1 (Chen et al., Proc Natl Acad Sci USA 94: 1914-8 (1997)). On the other hand, gene products which had been demonstrated to be specifically overexpressed in tumor cells, have been shown to be recognized as targets inducing cellular immune responses.
• Such gene products include p53 (Umano et al., Brit J Cancer 84: 1052-7 (2001)), HER2/ neu (Tanaka et al., Brit J Cancer 84: 94-9 (2001)), CEA (Nukaya et al., Int J Cancer 80: 92-7 (1999)), and so on.
• TAAs In spite of significant progress in basic and clinical research concerning TAAs (Rosenbeg et al., Nature Med 4: 321-7 (1998); Mukherji et al., Proc Natl Acad Sci USA 92: 8078-82 (1995); Hu et al., Cancer Res 56: 2479-83 (1996)), only limited number of candidate TAAs for the treatment of adenocarcinomas, including colorectal cancer, are available. TAAs abundantly expressed in cancer cells, and at the same time which expression is restricted to cancer cells would be promising candidates as inimuno therapeutic targets.
• PBMCs peripheral blood mononuclear cells
• HLA-A24 and HLA-A0201 are one of the popular HLA alleles in Japanese, as well as Caucasian (Date et al., Tissue Antigens 47: 93-101 (1996); Kondo et al., J Immunol 155: 4307-12 (1995); Kubo et al., J Immunol 152: 3913-24 (1994); Imanishi et al., Proceeding of the eleventh International Hictocompatibility Workshop and Conference Oxford University Press, Oxford, 1065 (1992); Williams et al., Tissue Antigen 49: 129 (1997)).
• antigenic peptides of carcinomas presented by these HLAs may be especially useful for the treatment of carcinomas among Japanese and Caucasian.
• the invention is based on the discovery of a pattern of gene expression correlated with pancreatic cancer (PNC).
• PNC pancreatic cancer
• the genes that are differentially expressed in pancreatic cancer are collectively referred to herein as "PNC nucleic acids” or “PNC polynucleotides” and the corresponding encoded polypeptides are referred to as “PNC polypeptides” or "PNC proteins.”
• the invention features a method of diagnosing or determining a predisposition to pancreatic cancer in a subject by determining an expression level of a PNC- associated gene in a patient derived biological sample, such as tissue sample.
• PNC- associated gene is meant a gene that is characterized by an expression level which differs in a cell obtained from a PNC cell compared to a normal cell.
• a normal cell is one obtained from pancreas tissue.
• a PNC-associated gene is one or more of PNC 1-605.
• An alteration, e.g., increase or decrease of the level of expression of the gene compared to a normal control level of the gene indicates that the subject suffers from or is at risk of developing PNC.
• control level is meant a level of gene expression detected in a normal, healthy individual or in a population of individuals known not to be suffering from pancreatic cancer.
• a control level is a single expression pattern derived from a single reference population or from a plurality of expression patterns.
• the control level can be a database of expression patterns from previously tested cells.
• a normal individual is one with no clinical symptoms of pancreatic cancer.
• PNC control level is meant the expression profile of the PNC-associated genes found in a population suffering from PNC.
• Gene expression is increased or decreased 10%, 25%, 50% compared to the control level. Alternately, gene expression is increased or decreased 1, 2, 5 or more fold compared to the control level. Expression is determined by detecting hybridization, e.g. , on an array, of a PNC-associated gene probe to a gene transcript of the patient-derived tissue sample.
• the patient derived tissue sample is any tissue from a test subject, e.g., a patient known to or suspected of having PNC.
• the tissue contains an epithelial cell.
• the tissue is an epithelial cell from a pancreatic ductal adenocarcinoma.
• the invention also provides a PNC reference expression profile of a gene expression level of two or more of PNC 1-605.
• the invention provides a PNC reference expression profile of the levels of expression two or more of PNC 1-259 or PNC 260-605.
• the invention further provides methods of identifmg an agent that inhibits or enhances the expression or activity of a PNC-associated gene, e.g. PNC 1-605 by contacting a test cell expressing a PNC-associated gene with a test agent and determining the expression level of the PNC associated gene.
• the test cell is a epithelial cell such as an epithelial cell from a pancreatic adenocarcinoma.
• a decrease of the level compared to a normal control level of the gene indicates that the test agent is an inhibitor of the PNC-associated gene and reduces a symptom of PNC, e.g. PNC 1-259.
• an increase of the level or activity compared to a normal control level or activity of the gene indicates that said test agent is an enhancer of expression or function of the PNC-associated gene and reduces a symptom of PNC, e.g, PNC 260-605.
• the invention also provides a kit with a detection reagent which binds to one or more PNC nucleic acids or which binds to a gene product encoded by the nucleic acid sequences. Also provided is an array of nucleic acids that binds to one or more PNC nucleic acids.
• Therapeutic methods include a method of treating or preventing pancreatic cancer in a subject by administering to the subject an antisense composition.
• the antisense composition reduces the expression of a specific target gene, e.g., the antisense composition contains a nucleotide, which is complementary to a sequence selected from the group consisting of PNC 1-259.
• Another method includes the steps of administering to a subject an short interfering RNA (siRNA) composition.
• the siRNA composition reduces the expression of a nucleic acid selected from the group consisting of PNC 1-259.
• treatment or prevention of PNC in a subject is carried out by administering to a subject a ribozyme composition.
• the nucleic acid-specific ribozyme composition reduces the expression of a nucleic acid selected from the group consisting of PNC 1-259.
• Other therapeutic methods include those in which a subject is administered a compound that increases the expression of PNC 260-605 or activity of a polypeptide encoded by PNC 260-605.
• the invention also includes vaccines and vaccination methods.
• a method of treating or preventing PNC in a subject is carried out by administering to the subject a vaccine containing a polypeptide encoded by a nucleic acid selected from the group consisting of PNC 1-259 or an immunologically active fragment such a polypeptide.
• An immunologically active fragment is a polypeptide that is shorter in length than the full-length naturally-occurring protein and which induces an immune response.
• an immunologically active fragment at least 8 residues in length and stimulates an immune cell such as a T cell or a B cell. L-nmune cell stimulation is measured by detecting cell proliferation, elaboration of cytokines (e.g., IL-2), or production of an antibody.
• cytokines e.g., IL-2
• the present invention provides target molecules for treating or preventing malignant pancreatic cancer.
• 76 PNC 606- 681
• 168 PNC 682-849
• 84 850-933 genes were identified as genes that showed unique altered expression patterns in pancreatic cancer cells with lymph-node metastasis, liver metastasis and early recurrence, respectively.
• malignant pancreatic cancer can be treated or prevented via the suppression of the expression or activity of up-regulated genes selected from the group consisting of PNC 606-640 and PNC 682-741.
• recurrence of pancreatic cancer can be treated or prevented via the suppression of the expression or activity of up-regulated genes selected from the group consisting of PNC 850- 893.
• malignant pancreatic cancer can also be treated or prevented through enhancing the expression or activity of down-regulating genes in cancerous cells.
• the present invention also provides methods for predicting recurrence of pancreatic cancer.
• the method comprises the step of measuring the expression level of marker genes selected from the group consisting of PNC 850-879.
• the marker genes were identified as genes that show unique altered expression patterns in pancreatic cancer cells of patients with recurrence within 12 month after surgery. Therefore, recurrence of the pancreatic cancer in a subject can be predicted by determining whether the expression level detected in a sample derived from the subject is closer to the mean expression level of early- recurrent cases or late-recurrent cases in reference samples.
• Figure 1 A is a photograph of a hematoxylin and eosin stained pancreatic cancer
• 1A1 is the same sections after microdissection.
• 1 A2 is a photograph of the microdissected cancer cells captured on the collecting cap.
• Figure IB is a photograph of a hematoxylin and eosin stained pancreatic cancer (scirrhous type) before microdissection.
• IB 1 is the same sections after microdissection.
• 1B2 is a photograph of the microdissected cancer cells captured on the collecting cap.
• Figure 1C is a photograph of normal pancreas containing greater than 90% acinar cell.
• Figure ID is a photograph of microdissected normall pancreatic ductal epithial cells.
• Figure 2 is a photograph of a DNA agarose gel showing expression of representative 12 genes and TUBA examined by semi-quantitative RT-PCR using cDNA prepared from amplified RNA. Lanes 1-12 each show the expression level of the genes in a different PNC patient. Gene symbols are noted for the genes. The last lane shows the expression level of each gene in a normal individual.
• Figure 3 Dendrogram of two-dimensional hierarchical clustering analysis using 76 genes selected by a random-permutation test which compared expression profiles of 9 lymph-node positive cases with those of 4 lymph-node negative cases. In the vertical axis, 35 genes were clustered in the upper branch, indicating relatively high levels of expression in lymph-node positive cases.
• Figure 4 Dendrogram of two-dimensional hierarchical clustering analysis using 168 genes selected by a random-permutation test which compared expression profiles of 5 liver-metastasis-positive cases with those of 6 negative cases. In the vertical axis, 60 genes were clustered in the upper branch which was more highly expressed in liver-metastasis- positive cases.
• FIG. 5 (A) Result of a two-dimensional hierarchical clustering analysis using 84 genes selected by a random-permutation test which compared expression profiles of 7 early-recurrent cases (within 12months after surgery) with those of 6 late-recurrent cases (over 12 months after surgery). In the vertical axis, 84 genes were clustered in different branches according to similarity in relative expression ratios.
• C Different prediction scores appear when the number of discriminating genes is changed. Red diamonds represent early-recurrent cases; blue diamonds denote late-recurrent cases.
• pancreatic ductal adenocarcinoma has a characteristic of highly desmoplastic stromal reaction, only a low percentage (about 30%) of cancer cells are contained in the tumor mass. Furthermore, normal pancreatic ductal epithelial cells, which recently considered to be the normal counterpart of the pancreatic adenocarcinoma, occupied only less than 5% of the total population of cells composing the organ 'pancreas' (7, 8 ). Hence, the gene-expression analysis of PNC compared to normal pancreas by using whole tissue is distorted by the contamination of needless cells such as fibroblast, inflammatory cells, acinar cells, etc., and results in "noisy data”. Therefore Laser capture microdissection (LCM), or Laser microbeam microdissection (LMM), a method for isolating pure cell populations, was used to obtain specific cancer cells and normal epithelial cells (9,10).
• LCM Laser capture microdissection
• LMM Laser microbeam microdissection
• the present invention is based in part on the discovery of changes in expression patterns of multiple nucleic acids in epithelial cells from adenocarcinomas of patients with PNC.
• the differences in gene expression were identified by using a comprehensive cDNA microarray system.
• the gene-expression profiles of cancer cells from 18 PNCs were analyzed using cDNA microarray representing 23,040 genes couples with laser microdissection.
• 259 genes were identified as commonly up-regulated in PNC cells
• 346 genes were identified as being commonly down-regulated in PNC cells.
• selection was made of candidate molecular markers with the potential of detecting cancer-related proteins in serum or sputum of patients, and discovered some potential targets for development of signal-suppressing strategies in human PNC.
• differentially expressed genes identified herein are used for diagnostic purposes as markers of PNC and as gene targets, the expression of which is altered to treat or alleviate a symptom of PNC.
• PNC-associated genes The genes whose expression levels are modulated (i.e., increased or decreased) in PNC patients are summarized in Tables 3-4 and are collectively referred to herein as " PNC- associated genes " , "PNC nucleic acids” or “PNC polynucleo tides” and the corresponding encoded polypeptides are referred to as “PNC polypeptides” or “PNC proteins.” Unless indicated otherwise, "PNC” is meant to refer to any of the sequences disclosed herein, (e.g., PNC 1-605). The genes have been previously described and are presented along with a database accession number.
• PNC By measuring expression of the various genes in a sample of cells, PNC is diagnosed. Similarly, measuring the expression of these genes in response to various agents can identify agents for treating PNC.
• the invention involves determining (e.g., measuring) the expression of at least one, and up to all the PNC sequences listed in Tables 3-4.
• sequence information provided by the GeneBankTM database entries for the known sequences the PNC-associated genes are detected and measured using techniques well known to one of ordinary skill in the art.
• sequences within the sequence database entries corresponding to PNC sequences are used to construct probes for detecting PNC RNA sequences in, e.g., northern blot hybridization analysis. Probes include at least 10, 20, 50, 100, 200 nucleotides of a reference sequence.
• the sequences can be used to construct primers for specifically amplifying the PNC nucleic acid in, e.g, amplification-based detection methods such as reverse-transcription based polymerase chain reaction.
• Expression level of one or more of the PNC-associated genes in the test cell population is then compared to expression levels of the some genes in a reference population.
• the reference cell population includes one or more cells for which the compared parameter is known, i. e. , pancreatic ductal adenocarcinoma cells or normal pancreatic ductal epithelial cells.
• a pattern of gene expression levels in the test cell population compared to the reference cell population indicates PNC or predisposition thereto depends upon the composition of the reference cell population. For example, if the reference cell population is composed of non-PNC cells, a similar gene expression pattern in the test cell population and reference cell population indicates the test cell population is non-PNC. Conversely, if the reference cell population is made up of PNC cells, a similar gene expression profile between the test cell population and the reference cell population indicates that the test cell population includes PNC cells.
• a level of expression of a PNC marker gene in a test cell population is considered altered in levels of expression if its expression level varies from the reference cell population by more than 1.0, 1.5, 2.0, 5.0, 10.0 or more fold from the expression level of the corresponding PNC marker gene in the reference cell population.
• control nucleic acid e.g. a housekeeping gene.
• a control nucleic acid is one which is known not to differ depending on the cancerous or non- cancerous state of the cell. Expression levels of the control nucleic acid in the test and reference nucleic acid can be used to normalize signal levels in the compared populations.
• Control genes include, e.g. ⁇ -actin, glyceraldehyde 3- phosphate dehydrogenase or ribosomal protein PI.
• the test cell population is compared to multiple reference cell populations. Each of the multiple reference populations may differ in the known parameter. Thus, a test cell population may be compared to a second reference cell population known to contain, e.g., PNC cells, as well as a second reference population known to contain, e.g., non-PNC cells (normal cells).
• the test cell is included in a tissue type or cell sample from a subject known to contain, or to be suspected of containing, PNC cells.
• the test cell is obtained from a bodily tissue or a bodily fluid, e.g., biological fluid
• the test cell is purified from pancreas tissue.
• the test cell population comprises an epithelial cell.
• the epithelial cell is from tissue known to be or suspected to be a pancreatic ductal adenocarcinoma.
• Cells in the reference cell population are derived from a tissue type as similar to test cell.
• the reference cell population is a cell line, e.g. a PNC cell line (positive control) or a normal non-PNC cell line (negative control).
• the control cell population is derived from a database of molecular information derived from cells for which the assayed parameter or condition is known.
• the subject is preferably a mammal.
• the mammal can be, e.g., a human, non-human primate, mouse, rat, dog, cat, horse, or cow.
• Expression of the genes disclosed herein is determined at the protein or nucleic acid level using methods known in the art. For example, Northern hybridization analysis using probes which specifically recognize one or more of these nucleic acid sequences can be used to determine gene expression. Alternatively, expression is measured using reverse- transcription-based PCR assays, e.g., using primers specific for the differentially expressed gene sequences. Expression is also determined at the protein level, i.e., by measuring the levels of polypeptides encoded by the gene products described herein, or biological activity thereof. Such methods are well known in the art and include, e.g., immunoassays based on antibodies to proteins encoded by the genes. The biological activity of the proteins encoded by the genes are also well known.
• PNC is diagnosed by measuring the level of expression of one or more PNC nucleic acid sequences from a test population of cells, (i.e., a patient derived biological sample).
• the test cell population contains an epithelial cell, e.g., a cell obtained from pancreas tissue.
• Gene expression is also measured from blood or other bodily fluids such as urine.
• Other biological samples can be used for measuring the protein level.
• the protein level in the blood, serum, or pancreatic juice derived from subject to be diagnosed can be measured by immunoassay or biological assay.
• PNC-associated genes e.g., PNC 1-605 is determined in the test cell or biological sample and compared to the expression of the normal control level.
• a normal control level is an expression profile of a PNC-associated gene typically found in a population known not to be suffering from PNC.
• An increase or a decrease of the level of expression in the patient derived tissue sample of the PNC-associated genes indicates that the subject is suffering from or is at risk of developing PNC.
• an increase in expression of PNC 1-259 in the test population compared to the normal control level indicates that the subject is suffering from or is at risk of developing PNC.
• a decrease in expression of PNC 260-605 in the test population compared to the normal control level indicates that the subject is suffering from or is at risk of developing PNC.
• PNC-associated genes When one or more of the PNC-associated genes are altered in the test population compared to the normal control level indicates that the subject suffers from or is at risk of developing PNC. For example, at least 1%, 5%, 25%, 50%, 60%, 80%, 90% or more of the panel of PNC-associated genes (PNC 1-259, PNC 260-605, or PNC 1-605) are altered.
• the present invention provides a method for predicting prognosis of PNC in a subject, the method comprising the steps of: (a) detecting an expression level of one or more marker genes in a specimen collected from a subject to be predicted, wherein the one or more marker genes are selected from the group consisting of PNC 850-866, 894-906; and (b) comparing the expression level of the one or more marker genes to that of a early recurrence cases and late recurrence cases; and (c) when the expression level of one or marker genes is close to that of the early recurrence case, determining the subject to be at a risk of having recurrence of PNC and when the expression level of one or marker genes is close to that of the late recurrence case, determining the risk of the subject of having recurrence of PNC to be low.
• marker gene(s) for prediction of prognosis of PNC may be at least one gene selected from the group consisting of PNC 850-933 ; 84 genes shown in Table ⁇ .
• the nucleotide sequences of the genes and amino acid sequences encoded thereby are known in the art. See Table 8 for the Accession Numbers of the genes.
• prediction of prognosis comprises prediction of probability for recurrence of PNC.
• the subject is determined to have poor prognosis.
• the expression levels of multiple marker genes selected from the group of PNC 850-866, 894-906 can be measured for the prediction.
• the 30 genes consisting of top 17 genes (ARGBP2, CBARAl, EEF1G, LCAT, RPL23A, RPL17, ATP1A1, QARS, BZRP, TUFM, SERPINA4, SCAP, HK1, RPS11, SYNGR2, FLOT2, PSMB4) of up-regulated in late recurrence cases genes and top 13 genes of up-regulated in early recurrence cases genes (MTMR1, HT010, NPD002, YME1L1, CCT6A, HSPD1, TIMM9, GRB14, FLJ10803, LAMP1, MLLT4, CTSB, RALY) of Table 8 are useful for the prediction.
• the specimen is collected from a subject.
• Preferable specimen include pancreatic tissue derived from patient of pancreatic cancer.
• Methods for measuring the expression level of marker genes are well-known in the art.
• DNA array is useful for measuring the expression level of multiple marker genes. According to the present invention, first, the expression level of each marker genes in a specimen is measured and then compared to that of early recurrence cases and late recurrence cases. The expression level of the marker genes of each of the cases can be measured prior to the comparison of the expression level.
• the recurrence of PNC can be predicted using prediction score that may be calculated by statistical methods. Methods for calculating prediction score is well- known in the art (T.R. Golub et al., Science 286, 531-7, 1999 ; TJ. MacDonald et al., Nat.
• prediction of recurrence using prediction score in the present invention may be also performed according to the method disclosed in the Example.
• An agent that inhibits the expression or activity of a PNC-associated gene is identified by contacting a test cell population expressing a PNC-associated up-regulated gene with a test agent and determining the expression level of the PNC-associated gene. A decrease in expression in the presence of the agent compared to the normal control level (or compared to the level in the absence of the test agent) indicates the agent is an inhibitor of a PNC- associated up-regulated gene and useful to inhibit PNC.
• an agent that enhances the expression or activity of a PNC-associated down-regulated gene is identified by contacting a test cell population expressing a PNC- associated gene with a test agent and determining the expression level or activity of the PNC- associated down-regulated gene. An increase of expression or activity compared to a normal control expression level or activity of the PNC-associated gene indicates that the test agent augments expression or activity of the PNC-associated down-regulated gene.
• the test cell population is any cell expressing the PNC-associated genes.
• the test cell population contains an epithelial cell, such as a cell is or derived from pancreas tissue.
• the test cell is an immortalized cell line derived from an adenocarcinoma cell.
• the test cell is a cell, which has been transfec ted with a PNC-associated gene or which has been transfected with a regulatory sequence (e.g. promoter sequence) from a PNC-associated gene operably linked to a reporter gene.
• a regulatory sequence e.g. promoter sequence
• the differentially expressed PNC-associated gene identified herein also allow for the course of treatment of PNC to be monitored.
• a test cell population is provided from a subject undergoing treatment for PNC. If desired, test cell populations are obtained from the subject at various time points before, during, or after treatment. Expression of one or more of the PNC-associated gene, in the cell population is then determined and compared to a reference cell population which includes cells whose PNC state is known. The reference cells have not been exposed to the treatment.
• the reference cell population contains no PNC cells, a similarity in expression between PNC-associated gene in the test cell population and the reference cell population indicates that the treatment is efficacious. However, a difference in expression between PNC- associated gene in the test population and a normal control reference cell population indicates a less favorable clinical outcome or prognosis.
• efficacious is meant that the treatment leads to a reduction in expression of a pathologically up-regulated gene, increase in expression of a pathologically down-regulated gene or a decrease in size, prevalence, or metastatic potential of pancreatic ductal adenocarcinoma in a subject.
• effcacious means that the treatment retards or prevents a pancreatic tumor from forming or retards, prevents, or alleviates a symptom of clinical PNC. Assessment of pancreatic tumors is made using standard clinical protocols.
• Efficaciousness is determined in association with any known method for diagnosing or treating PNC.
• PNC is diagnosed for example, by identifying symptomatic anomalies, e.g., weight loss, abdominal pain, back pain, anorexia, nausea, vomiting and generalized malaise, weakness, and jaundice.
• An agent that is metabolized in a subject to act as an anti-PNC agent can manifest itself by inducing a change in gene expression pattern in the subject's cells from that characteristic of a cancerous state to a gene expression pattern characteristic of a non-cancerous state.
• the differentially expressed PNC- associated gene disclosed herein allow for a putative therapeutic or prophylactic inhibitor of PNC to be tested in a test cell population from a selected subject in order to determine if the agent is a suitable inhibitor of PNC in the subject.
• a test cell population from the subject is exposed to a therapeutic agent, and the expression of one or more of PNC 1-605 genes is determined.
• the test cell population contains a PNC cell expressing a PNC-associated gene.
• the test cell is an epithelial cell.
• a test cell population is incubated in the presence of a candidate agent and the pattern of gene expression of the test sample is measured and compared to one or more reference profiles, e.g., a PNC reference expression profile or a non-PNC reference expression profile.
• a decrease in expression of one or more of PNC 1-259 or an increase in expression of one or more of PNC 260-605 in a test cell population relative to a reference cell population containing PNC is indicative that the agent is therapeutic.
• test agent can be any compound or composition.
• test agents are immunomodulatory agents.
• Screening assays for identifying therapeutic agents The differentially expressed genes disclosed herein can also be used to identify candidate therapeutic agents for treating PNC.
• the method is based on screening a candidate therapeutic agent to determine if it converts an expression profile of PNC 1-605 characteristic of a PNC state to a pattern indicative of a non-PNC state.
• a cell is exposed to a test agent or a combination of test agents (sequentially or consequentially) and the expression of one or more PNC 1-605 in the cell is measured.
• the expression profile of the PNC-associated gene in the test population is compared to expression level of the PNC-associated gene in a reference cell population that is not exposed to the test agent.
• An agent effective in stimulating expression of under-expressed genes, or in suppressing expression of over-expressed genes is deemed to lead to a clinical benefit such compounds are further tested for the ability to prevent pancreatic ductal adenocarcmomal growth in animals or test subjects.
• the present invention provides methods for screening candidate agents which are potential targets in the treatment of PNC.
• candidate agents which are potential targets in the treatment of PNC, can be identified through screenings that use the expression levels and activities of marker genes as indices.
• screening may comprise, for example, the following steps: a) contacting a test compound with a polypeptide encoded by PNC 1-605; b) detecting the binding activity between the polypeptide and the test compound; and c) selecting a compound that binds to the polypeptide.
• the screening method of the present invention may comprise the following steps: a) contacting a candidate compound with a cell expressing one or more marker genes, wherein the one or more marker genes is selected from the group consisting of PNC
• Cells expressing a marker gene include, for example, cell lines established from PNC; such cells can be used for the above screening of the present invention.
• the screening method of the present invention may comprise the following steps: a) contacting a test compound with a polypeptide encoded by selected from the group consisting of PNC 1-605; b) detecting the biological activity of the polypeptide of step (a); and c) selecting a compound that suppresses the biological activity of the polypeptide encoded by PNC 1-259 in comparison with the biological activity detected in the absence of the test compound, or enhances the biological activity of the polypeptide encoded by PNC 260-605 in comparison with the biological activity detected in the absence of the test compound.
• a protein required for the screening can be obtained as a recombinant protein using the nucleotide sequence of the marker gene. Based on the information of the marker gene, one skilled in the art can select any biological activity of the protein as an index for screening and a measurement method based on the selected biological activity.
• the screening method of the present invention may comprise the following steps: a) contacting a candidate compound with a cell into which a vector comprising the transcriptional regulatory region of one or more marker genes and a reporter gene that is expressed under the control of the transcriptional regulatory region has been introduced, wherein the one or more marker genes are selected from the group consisting of PNC 1-605 b) measuring the activity of said reporter gene; and c) selecting a compound that reduces the expression level of said reporter gene when said marker gene is an up-regulated marker gene selected from the group consisting of PNC 1-259 or that enhances the expression level of said reporter gene when said marker gene is a down-regulated marker gene selected from the group consisting of
• Suitable reporter genes and host cells are well known in the art.
• the reporter construct required for the screening can be prepared by using the transcriptional regulatory region of a marker gene.
• a reporter construct can be prepared by using the previous sequence information.
• a nucleotide segment containing the transcriptional regulatory region can be isolated from a genome library based on the nucleotide sequence information of the marker gene.
• the compound isolated by the screening is a candidate for drugs that inhibit the activity of the protein encoded by marker genes and can be applied to the treatment or prevention of pancreatic cancer.
• compound in which a part of the structure of the compound inhibiting the activity of proteins encoded by marker genes is converted by addition, deletion and/or replacement are also included in the compounds obtainable by the screening method of the present invention.
• the isolated compound When administrating the compound isolated by the method of the invention as a pharmaceutical for humans and other mammals, such as mice, rats, guinea-pigs, rabbits, cats, dogs, sheep, pigs, cattle, monkeys, baboons, and chimpanzees, the isolated compound can be directly administered or can be formulated into a dosage form using known pharmaceutical preparation methods.
• the drugs can be taken orally, as sugar-coated tablets, capsules, elixirs and microcapsules, or non-orally, in the form of injections of sterile solutions or suspensions with water or any other pharmaceutically acceptable liquid.
• the compounds can be mixed with pharmaceutically acceptable carriers or media, specifically, sterilized water, physiological saline, plant-oils, emulsifiers, suspending agents, surfactants, stabilizers, flavoring agents, excipients, vehicles, preservatives, binders, and such, in a unit dose form required for generally accepted drug implementation.
• the amount of active ingredients in these preparations makes a suitable dosage within the indicated range acquirable.
• additives that can be mixed to tablets and capsules are, binders such as gelatin, corn starch, tragacanth gum and arabic gum; excipients such as crystalline cellulose; swelling agents such as corn starch, gelatin and alginic acid; lubricants such as magnesium stearate; sweeteners such as sucrose, lactose or saccharin; and flavoring agents such as peppermint, Gaultheria adenothrix oil and cherry.
• a liquid carrier such as an oil, can also be further included in the above ingredients.
• Sterile composites for injections can be formulated following normal drug implementations using vehicles such as distilled water used for injections.
• Physiological saline, glucose, and other isotonic liquids including adjuvants can be used as aqueous solutions for injections.
• adjuvants such as D-sorbitol, D-mannnose, D-mannitol, and sodium chloride
• Suitable solubilizers such as alcohol, specifically ethanol, polyalcohols such as propylene glycol and polyethylene glycol, non-ionic surfactants, such as Polysorbate 80 (TM) and HCO-50.
• Sesame oil or Soy-bean oil can be used as a oleaginous liquid and may be used in conjunction with benzyl benzoate or benzyl alcohol as a solubilizer and may be formulated with a buffer, such as phosphate buffer and sodium acetate buffer; a pain-killer, such as procaine hydrochloride; a stabilizer, such as benzyl alcohol andphenol; and an anti-oxidant.
• the prepared injection may be filled into a suitable ampule.
• Methods well known to one skilled in the art may be used to administer the pharmaceutical composition of the present inevntion to patients, for example as intraarterial, intravenous, or percutaneous injections and also as intranasal, transbronchial, intramuscular or oral administrations.
• the dosage and method of administration vary according to the body- weight and age of a patient and the administration method; however, one skilled in the art can routinely select a suitable metod of administration. If said compound is encodable by a DNA, the DNA can be inserted into a vector for gene therapy and the vector administered to a patient to perform the therapy.
• the dosage and method of administration vary according to the body- weight, age, and symptoms of the patient but one skilled in the art can suitably select them.
• the dose of a compound that binds to the protein of the present invention and regulates its activity depends on the symptoms, the dose is about 0.1 mg to about 100 mg per day, preferably about 1.0 mg to about 50 mg per day and more preferably about 1.0 mg to about 20 mg per day, when administered orally to a normal adult (weight 60 kg).
• malignant cancer includes cancers having properties such as follows:
• malignant pancreatic cancer includes pancreatic cancer with metastasis.
• Screening assay for malignant PNC of the present invention can be performed according to the mehtod for PNC described above using marker genes for malignant pancreatic cancer.
• marker genes selected from the group consisting of PNC 606- 681, and 682-849 are useful for the screening.
• 76 genes shown in Table 6 (PNC 606-681) were associated with lymph node metastasis.
• 35 genes (PNC 606-640) were relatively up-regulated and 41 genes (PNC 641-681) were down-regulated in node- positive tumors ( Figure 3).
• 168 genes (PNC 682-849) showed unique altered expression patterns in pancreatic cells with liver metastasis (Table 7) wherein 60 of the genes(PNC 682-741) were relatively up-regulated ( Figure 4).
• An agent suppressing the activity or expression of these up-regulated genes obtained by the present invention are useful for treating or preventing malignant pancreatic cancer with lymph-node metastasis or liver metastasis.
• an agent enhancing the activity or expression of the down- regulated genes obtained by the present invention are also useful for treating or preventing malignant pancreatic cancer.
• the present invention provides target molecules for treating or preventing recurrence of pancreatic cancer.
• recurrence of pancreatic cancer indicates recurrence of cancer in pancreas after surgery.
• the recurrence of cancer within 12 month after surgery can be predicted by the invention.
• early recurrence includes the recurrence within 12 month after surgery, and when no recurrence can be observed within 12 month after surgery in a case, the case is considered to be a pancreatic cancer with "late recurrence”.
• 84 genes (PNC 850-933) shown in Table 8 are useful as the marker genes for the screening of the present invention.
• the genes shown in Figure 5A-1 are up-regulated in early recurrence cases(PNC 894-933), and the genes shown in Figure 5A-2 are up-regulated in late recurrence cases(PNC 850-893). Therefore, an agent suppressing the up-regulated genes in early recurrence cases is useful for treating or preventing recurrence. Alternatively, an agent enhancing the up-regulated genes in late recurrence cases is also useful for treating or preventing recurrence.
• comparing gene expression of one or more PNC-associated gene in the test cell population and the reference cell population(s), or by comparing the pattern of gene expression over time in test cell populations derived from the subject the prognosis of the subject can be assessed.
• a decrease in expression of one or more of PNC 260-605 compared to a normal control or an increase of expression of one or more of PNC 1-259 compared to a normal control indicates less favorable prognosis.
• a similar expression of one or more of PNC 1-605 indicates a more favorable prognosis compared to nomal control indicates a more favorable prognosis for the subject.
• the prognosis of a subject can be assessed by comparing the expression profile of PNC 1-605.
• the classification score (CS) may be use for the comparing the expression profile.
• the invention also includes a PNC-detection reagent, e.g., a nucleic acid that specifically binds to or identifies one or more PNC nucleic acids such as oligonucleotide sequences, which are complementary to a portion of a PNC nucleic acid or antibodies which bind to proteins encoded by a PNC nucleic acid.
• the reagents are packaged together in the form of a kit.
• the reagents are packaged in separate containers, e.g., a nucleic acid or antibody (either bound to a solid matrix or packaged separately with reagents for binding them to the matrix), a control reagent (positive and/or negative), and/or a detectable label.
• Instructions e.g., written, tape, VCR, CD-ROM, etc.
• the assay format of the kit is a Northern hybridization or a sandwich ELISA known in the art.
• PNC detection reagent is immobilized on a solid matrix such as a porous strip to form at least one PNC detection site.
• the measurement or detection region of the porous strip may include a plurality of sites containing a nucleic acid.
• a test strip may also contain sites for negative and/or positive controls. Alternatively, control sites are located on a separate strip from the test strip.
• the different detection sites may contain different amounts of immobilized nucleic acids, i.e., a higher amount in the first detection site and lesser amounts in subsequent sites.
• the number of sites displaying a detectable signal provides a quantitative indication of the amount of PNC present in the sample.
• the detection sites may be configured in any suitably detectable shape and are typically in the shape of a bar or dot spanning the width of a teststrip.
• the kit contains a nucleic acid substrate array comprising one or more nucleic acids.
• the nucleic acids on the array specifically identify one or more nucleic acid sequences represented by PNC 1-605.
• the expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 40 or 50 or more of the nucleic acids represented by PNC 1-605 are identified by virtue of the level of binding to an array test strip or chip.
• the substrate array can be on, e.g., a. solid substrate, e.g., a "chip" as described in U.S. Patent No.5,744,305.
• the invention also includes a nucleic acid substrate array comprising one or more nucleic acids.
• the nucleic acids on the array specifically correspond to one or more nucleic acid sequences represented by PNC 1-605.
• the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 40 or 50 or more of the nucleic acids represented by PNC 1-605 are identified by detecting nucleic acid binding to the array.
• the invention also includes an isolated plurality (i.e., a mixture if two or more nucleic acids) of nucleic acids.
• the nucleic acids are in a liquid phase or a solid phase, e.g., immobilized on a solid support such as a nitrocellulose membrane.
• the plurality includes one or more of the nucleic acids represented by PNC 1-605. In various embodiments, the plurality includes 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 40 or 50 or more of the nucleic acids represented by PNC 1 -605.
• the invention provides a method for treating or alleviating a symptom of PNC in a subject by decreasing expression or activity of PNC 1-259 or increasing expression or activity of PNC 260-605.
• Therapeutic compounds are administered prophylactically or therapeutically to subject suffering from or at risk of (or susceptible to) developing PNC.
• Therapeutic agents include inhibitors of cell cycle regulation, cell proliferation, and protein kinase activity.
• the therapeutic method includes increasing the expression, or function, or both of one or more gene products of genes whose expression is decreased ("under-expressed genes") in a PNC cell relative to normal cells of the same tissue type from which the PNC cells are derived.
• the subject is treated with an effective amount of a compound, which increases the amount of one or more of the under-expressed genes in the subject.
• Administration can be systemic or local.
• Therapeutic compounds include a polypeptide product of an under-expressed gene, or a biologically active fragment thereof a nucleic acid encoding an under-expressed gene and having expression control elements permitting expression in the PNC cells; for example an agent which increases the level of expression of such gene endogenous to the PNC cells (i.e., which up-regulates expression of the under- expressed gene or genes).
• Administration of such compounds counters the effects of aberrantly-under expressed of the gene or genes in the subject's pancreas cells and improves the clinical condition of the subject.
• the method also includes decreasing the expression, or function, or both, of one or more gene products of genes whose expression is aberrantly increased ("over-expressed gene") in pancreas cells.
• Expression is inhibited in any of several ways known in the art. For example, expression is inhibited by administering to the subject a nucleic acid that inhibits, or antagonizes, the expression of the over-expressed gene or genes, e.g., an antisense oligonucleotide or small interfering RNA which disrupts expression of the over-expressed gene or genes.
• antisense nucleic acids corresponding to the nucleotide sequence of PNC 1-259 can be used to reduce the expression level of the PNC 1-259.
• Antisense nucleic acids corresponding to PNC 1-259 that are up-regulated in pancreatic cancer are useful for the treatment of pancreatic cancer.
• the antisense nucleic acids of the present invention may act by binding to the PNC 1-259 or mRNAs corresponding thereto, thereby inhibiting the transcription or translation of the genes, promoting the degradation of the mRNAs, and/or inhibiting the expression of proteins encoded by the PNC 1-259, finally inhibiting the function of the proteins.
• antisense nucleic acids encompasses both nucleotides that are entirely complementary to the target sequence and those having a mismatch of one or more nucleotides, so long as the antisense nucleic acids can specifically hybridize to the target sequences.
• the antisense nucleic acids of the present invention include polynucleotides that have a homology of at least 70% or higher, preferably at 80% or higher, more preferably 90% or higher, even more preferably 95% or higher over a span of at least 15 continuous nucleotides. Algorithms known in the art can be used to determine the homology.
• the antisense nucleic acid derivatives of the present invention act on cells producing the proteins encoded by marker genes by binding to the DNAs or mRNAs encoding the proteins, inhibiting their transcription or translation, promoting the degradation of the mRNAs, and inhibiting the expression of the proteins, thereby resulting in the inhibition of the protein function.
• An antisense nucleic acid derivative of the present invention can be made into an external preparation, such as a liniment or a poultice, by mixing with a suitable base material which is inactive against the derivative.
• the derivatives can be formulated into tablets, powders, granules, capsules, liposome capsules, injections, solutions, nose-drops and freeze-drying agents by adding excipients, iso tonic agents, solubilizers, stabilizers, preservatives, pain-killers, and such. These can be prepared by following known methods.
• the antisense nucleic acids derivative is given to the patient by directly applying onto the ailing site or by injecting into a blood vessel so that it will reach the site of ailment.
• An antisense-mounting medium can also be used to increase durability and membrane- permeability. Examples are, liposomes, poly-L-lysine, lipids, cholesterol, lipofectin or derivatives of these.
• the dosage of the antisense nucleic acid derivative of the present invention can be adjusted suitably according to the patient's condition and used in desired amounts. For example, a dose range of 0.1 to 100 mg/kg, preferably 0.1 to 50 mg/kg can be administered.
• the antisense nucleic acids of the invention inhibit the expression of the protein of the invention and is thereby useful for suppressing the biological activity of a protein of the invention.
• expression-inhibitors, comprising the antisense nucleic acids of the invention are useful since they can inhibit the biological activity of a protein of the invention.
• the antisense nucleic acids of present invention include modified oligonucleotides.
• siRNA against marker gene can be used to reduce the expression level of the marker gene.
• siRNA is meant a double stranded RNA molecule which prevents translation of a target mRNA. Standard techniques of introducing siRNA into the cell are used, including those in which DNA is a template from which RNA is transcribed.
• the siRNA comprises a sense nucleic acid sequence and an anti-sense nucleic acid sequence against an up-regulated marker gene, such as PNC 1-259.
• the siRNA is constructed such that a single transcript has both the sense and complementary antisense sequences from the target gene, e.g., a hairpin.
• the method is used to alter the expression in a cell of an up-regulated, e.g., as a result of malignant transformation of the cells. Binding of the siRNA to a transcript corresponding to one of the PNC 1-259 in the target cell results in a reduction in the protein production by the cell.
• the length of the oligonucleotide is at least 10 nucleotides and may be as long as the naturally-occurring transcript.
• the oligonucleotide is 19-25 nucleotides in length.
• the oligonucleotide is less than 75, 50, 25 nucleotides in length.
• the nucleotide sequence of the siRNAs were designed using an siRNA design computer program available from the Ambion website (http://www.ambion.com techlib/ misc/siRNA_finder.html). The computer program selects nucleotide sequences for siRNA synthesis based on the following protocol. Selection of siRNA Target Sites: 1. Beginning with the AUG start codon of the object transcript, scan downstream for AA dinucleotide sequences. Record the occurrence of each AA and the 3' adjacent 19 nucleotides as potential siRNA target sites. Tuschl, et al. recommend against designing siRNA to the 5* and 3' untranslated regions (UTRs) and regions near the start codon (within 75 bases) as these may be richer in regulatory protein binding sites. UTR-binding proteins and/or translation initiation complexes may interfere with binding of the siRNA endonuclease complex.
• the homology search can be performed using BLAST, which can be found on the NCBI server at: www.ncbi.nlm.nih.gov/BLAST/
• the antisense oligonucleotide or siRNA of the invention inhibit the expression of the polypeptide of the invention and is thereby useful for suppressing the biological activity of the polypeptide of the invention.
• expression-inhibitors comprising the antisense oligonucleotide or siRNA of the invention, are useful in the point that they can inhibit the biological activity of the polypeptide of the invention. Therefore, a composition comprising the antisense oligonucleotide or siRNA of the present invention is useful in treating a pancreatic cancer.
• function of one or more gene products of the over-expressed genes is inhibited by administering a compound that binds to or otherwise inhibits the function of the gene products.
• the compound is an antibody which binds to the over-expressed gene product or gene products.
• the present invention refers to the use of antibodies, particularly antibodies against a protein encoded by an up-regulated marker gene, or a fragment of the antibody.
• antibody refers to an immunoglobulin molecule having a specific structure, that interacts (i.e., binds) only with the antigen that was used for synthesizing the antibody (i.e., the up-regulated marker gene product) or with an antigen closely related to it.
• an antibody may be a fragment of an antibody or a modified antibody, so long as it binds to one or more of the proteins encoded by the marker genes.
• the antibody fragment may be Fab, F(ab') , Fv, or single chain Fv (scFv), in which Fv fragments from H and L chains are ligated by an appropriate linker (Huston J. S. et al. Proc. Natl. Acad. Sci. U.S.A. 85:5879-5883 (1988)). More specifically, an antibody fragment may be generated by treating an antibody with an enzyme, such as papain or pepsin. Alternatively, a gene encoding the antibody fragment may be constructed, inserted into an expression vector, and expressed in an appropriate host cell (see, for example, Co M. S. et al. J. Immunol. 152:2968- 2976 (1994); Better M. and Horwitz A.
• An antibody may be modified by conjugation with a variety of molecules, such as polyethylene glycol (PEG).
• PEG polyethylene glycol
• the present invention provides such modified antibodies.
• the modified antibody can be obtained by chemically modifying an antibody. These modification methods are conventional in the field.
• an antibody may be obtained as a chimeric antibody, between a variable region derived from a nonhuman antibody and a constant region derived from a human antibody, or as a humanized antibody, comprising the complementarity determining region (CDR) derived from a nonhuman antibody, the frame work region (FR) derived from a human antibody, and the constant region.
• CDR complementarity determining region
• FR frame work region
• Cancer therapies directed at specific molecular alterations that occur in cancer cells have been validated through clinical development and regulatory approval of anti-cancer drugs such as trastuzumab (Herceptin) for the treatment of advanced breast cancer, imatinib methylate (Gleevec) for chronic myeloid leukemia, gefitinib (Iressa) for non-small cell lung cancer (NSCLC), and rituximab (anti-CD20 mAb) for B-cell lymphoma and mantle cell lymphoma (Ciardiello F, Tortora G.
• trastuzumab Herceptin
• Imatinib methylate for chronic myeloid leukemia
• gefitinib Iressa
• NSCLC non-small cell lung cancer
• rituximab anti-CD20 mAb
• targeted drugs can enhance the efficacy of standard chemotherapy when used in combination with it (Gianni L. (2002). Oncology, 63 Suppl 1, 47-56.; Klejman A, Rushen L, Morrione A, Slupianek A and Skorski T. (2002). Oncogene, 21, 5868-5876.). Therefore, future cancer treatments will probably involve combining conventional drugs with target-specific agents aimed at different characteristics of tumor cells such as angiogenesis and invasiveness.
• modulatory methods are performed ex vivo or in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g., by administering the agent to a subject).
• the method involves administering a protein or combination of proteins or a nucleic acid molecule or combination of nucleic acid, molecules as therapy to counteract aberrant expression or activity of the differentially expressed genes.
• Diseases and disorders that are characterized by increased (relative to a subject not suffering from the disease or disorder) levels or biological activity of the genes may be treated with therapeutics that antagonize (i.e., reduce or inhibit) activity of the over-expressed gene or genes.
• Therapeutics that antagonized activity are administered therapeutically or prophylactically.
• Therapeutics that may be utilized include, e.g., (i) a polypeptide, or analogs, derivatives, fragments or homologs thereof of the over-expressed or under-expressed gene or genes; (ii) antibodies to the over-expressed or under-expressed gene or genes; (iii) nucleic acids encoding the over-expressed or under-expressed gene or genes; (iv) antisense nucleic acids or nucleic acids that are "dysfunctional" (i.e., due to a heterologous insertion within the nucleic acids of one or more over-expressed or under-expressed gene or genes); (v) small interfering RNA (siRNA); or (vi) modulators (i.e., inhibitors, agonists and antagonists that alter the interaction between an over/under-expressed polypeptide and its binding partner).
• modulators i.e., inhibitors, agonists and antagonists that alter the interaction between an over/under-expressed polypeptide and its binding partner.
• the dysfunctional antisense molecules are utilized to "knockout" endogenous function of a polypeptide by homologous recombination (see, e.g., Capecchi, Science 244: 1288-1292 1989).
• 259 Diseases and disorders that are characterized by decreased (relative to a subject not suffering from the disease or disorder) levels or biological activity may be treated with therapeutics that increase (i.e., are agonists to) activity.
• Therapeutics that up-regulate activity may be administered in a therapeutic or prophylactic manner.
• Therapeutics that may be utilized include, but are not limited to, a polypeptide (or analogs, derivatives, fragments or homologs thereof) or an agonist that increases bioavailability.
• Increased or decreased levels can be readily detected by quantifying peptide and/or RNA, by obtaining a patient tissue sample (e.g., from biopsy tissue) and assaying it in vitro for RNA or peptide levels, structure and/or activity of the expressed peptides (or mRNAs of a gene whose expression is altered).
• tissue sample e.g., from biopsy tissue
• assaying it in vitro for RNA or peptide levels, structure and/or activity of the expressed peptides (or mRNAs of a gene whose expression is altered).
• Methods that are well-known within the art include, but are not limited to, immunoassays (e.g., by Western blot analysis, immunoprecipitation followed by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis, immunocytochemistry, etc.) and/or hybridization assays to detect expression of mRNAs (e.g., Northern assays, dot blots, in situ hybridization, etc.).
• immunoassays e.g., by Western blot analysis, immunoprecipitation followed by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis, immunocytochemistry, etc.
• hybridization assays to detect expression of mRNAs (e.g., Northern assays, dot blots, in situ hybridization, etc.).
• Prophylactic administration occurs prior to the manifestation of overt clinical symptoms of disease, such that a disease or disorder is prevented or, alternatively, delayed in its progression.
• Therapeutic methods include contacting a cell with an agent that modulates one or more of the activities of the gene products of the differentially expressed genes.
• An agent that modulates protein activity includes a nucleic acid or a protein, a naturally-occurring cognate ligand of these proteins, a peptide, a peptidomimetic, or other small molecule.
• the agent stimulates one or more protein activities of one or more of a differentially under- expressed gene.
• the present invention also relates to a method of treating or preventing pancreatic cancer in a subject comprising administering to said subject a vaccine comprising a polypeptide encoded by a nucleic acid selected from the group consisting of PNC 1-259 or an immunologically active fragment of said polypeptide, or a polynucleotide encoding the polypeptide or the fragment thereof.
• a vaccine comprising a polypeptide encoded by a nucleic acid selected from the group consisting of PNC 1-259 or an immunologically active fragment of said polypeptide, or a polynucleotide encoding the polypeptide or the fragment thereof.
• An administration of the polypeptide induces an anti- tumor immunity in a subject.
• a polypeptide encoded by a nucleic acid selected from the group consisting of PNC 1-259 or an immunologically active fragment of said polypeptide, or a polynucleotide encoding the polypeptide is administered.
• polypeptide or the immunologically active fragments thereof are useful as vaccines against PNC.
• the proteins or fragments thereof may be administered in a form bound to the T cell recepor (TCR) or presented by an antigen presenting cell (APC), such as macrophage, dendritic cell (DC), or B-cells. Due to the strong antigen presenting ability of DC, the use of DC is most preferable among the APCs.
• vaccine against PNC refers to a substance that has the function to induce anti-tumor immunity upon inoculation into animals.
• polypeptides encoded by PNC 1-259 or fragments thereof were suggested to be HLA-A24 or HL A- A* 0201 restricted epitopes peptides that may induce potent and specific immune response against PNC cells expressing PNC 1-259.
• the present invention also encompasses method of inducing anti-tumor immunity using the polypeptides.
• anti-tumor immunity includes immune responses such as follows: - induction of cytotoxic lymphocytes against tumors, - induction of antibodies that recognize tumors, and
• the protein when a certain protein induces any one of these immune responses upon inoculation into an animal, the protein is decided to have anti-tumor immunity inducing effect.
• the induction of the anti-tumor immunity by a protein can be detected by observing in vivo or in vitro the response of the immune system in the host against the protein.
• cytotoxic T lymphocytes For example, a method for detecting the induction of cytotoxic T lymphocytes is well known.
• a foreign substance that enters the living body is presented to T cells and B cells by the action of antigen presenting cells (APCs).
• APCs antigen presenting cells
• T cells that respond to the antigen presented by APC in antigen specific manner differentiate into cytotoxic T cells (or cytotoxic T lymphocytes; CTLs) due to stimulation by the antigen, and then proliferate (this is referred to as activation of T cells). Therefore, CTL induction by a certain peptide can be evaluated by presenting the peptide to T cell by APC, and detecting the induction of CTL.
• APC has the effect of activating CD4+ T cells, CD8+ T cells, macrophages, eosinophils, and NK cells. Since CD4+ T cells and CD 8+ T cells are also important in anti-tumor immunity, the anti-tumor immunity inducing action of the peptide can be evaluated using the activation effect of these cells as indicators.
• a method for evaluating the inducing action of CTL using dendritic cells (DCs) as APC is well known in the art.
• DC is a representative APC having the strongest CTL inducing action among APCs.
• the test polypeptide is initially contacted with DC, and then this DC is contacted with T cells. Detection of T cells having cytotoxic effects against the cells of interest after the contact with DC shows that the test polypeptide has an activity of inducing the cytotoxic T cells.
• Activity of CTL against tumors can be detected, for example, using the lysis of 51 Cr-labeled tumor cells as the indicator.
• the method of evaluating the degree of tumor cell damage using 3 H-thymidine uptake activity or LDH (lactose dehydrogenase)-release as the indicator is also well known.
• peripheral blood mononuclear cells may also be used as the APC.
• the induction of CTL is reported that it can be enhanced by culturing PBMC in the presence of GM-CSF and IL-4.
• CTL has been shown to be induced by culturing PBMC in the presence of keyhole limpet hemocyanin (KLH) and IL-7.
• KLH keyhole limpet hemocyanin
• test polypeptides confirmed to possess CTL inducing activity by these methods are polypeptides having DC activation effect and subsequent CTL inducing activity. Therefore, polypeptides that induce CTL against tumor cells are useful as vaccines against tumors. Furthermore, APC that acquired the ability to induce CTL against tumors by contacting with the polypeptides are useful as vaccines against tumors. Furthermore, CTL that acquired cytotoxicity due to presentation of the polypeptide antigens by APC can be also used as vaccines against tumors. Such therapeutic methods for tumors using anti-tumor immunity due to APC and CTL are referred to as cellular immunotherapy.
• the induction of anti-tumor immunity by a polypeptide can be confirmed by observing the induction of antibody production against tumors. For example, when antibodies against a polypeptide are induced in a laboratory animal immunized with the polypeptide, and when growth of tumor cells is suppressed by those antibodies, the polypeptide can be determined to have an ability to induce anti-tumor immunity.
• Anti-tumor immunity is induced by administering the vaccine of this invention, and the induction of anti-tumor immunity enables treatment and prevention of PNC.
• Therapy against cancer or prevention of the onset of cancer includes any of the steps, such as inhibition of the growth of cancerous cells, involution of cancer, and suppression of occurrence of cancer. Decrease in mortality of individuals having cancer, decrease of tumor markers in the blood, alleviation of detectable symptoms accompanying cancer, and such are also included in the therapy or prevention of cancer.
• Such therapeutic and preventive effects are preferably statistically significant. For example, in observation, at a significance level of 5% or less, wherein the therapeutic or preventive effect of a vaccine against cell proliferative diseases is compared to a control without vaccine administration. For example, Student's t- test, the Mann- Whitney U-test, or ANOVA may be used for statistical analyses.
• the above-mentioned protein having immunological activity or a vector encoding the protein may be combined with an adjuvant.
• An adjuvant refers to a compound that enhances the immune response against the protein when administered together (or successively) with the protein having immunological activity.
• adjuvants include cholera toxin, salmonella toxin, alum, and such, but are not limited thereto.
• the vaccine of this invention may be combined appropriately with a pharmaceutically acceptable carrier. Examples of such carriers are sterilized water, physiological saline, phosphate buffer, culture fluid, and such.
• the vaccine may contain as necessary, stabilizers, suspensions, preservatives, surfactants, and such.
• the vaccine is administered systemically or locally. Vaccine administration may be performed by single administration, or boosted by multiple administrations.
• tumors can be treated or prevented, for example, by the ex vivo method. More specifically, PBMCs of the subject receiving treatment or prevention are collected, the cells are contacted with the polypeptide ex vivo, and following the induction of APC or CTL, the cells may be administered to the subject.
• APC can be also induced by introducing a vector encoding the polypeptide into PBMCs ex vivo.
• APC or CTL induced in vitro can be cloned prior to administration. By cloning and growing cells having high activity of damaging target cells, cellular immunotherapy can be performed more effectively.
• APC and CTL isolated in this manner may be used for cellular immunotherapy not only against individuals from whom the cells are derived, but also against similar types of tumors from other individuals.
• a pharmaceutical composition for treating or preventing a cell proliferative disease, such as cancer, comprising a pharmaceutically effective amount of the polypeptide of the present invention is provided.
• the pharmaceutical composition may be used for raising anti tumor immunity.
• the present invention provides a method for treating or preventing malignant pancreatic cancer, or recurrence of pancreatic cancer by increasing or decreasing the expression or activity of marker genes.
• the marker genes that can be used for the treatment or prevention of malignant pancreatic cancer are PNC 606- 681 (Table 6) and PNC 682-849 (Table 7).
• the marker genes for treating or preventing the recurrence are PNC 850-933 (Table 8).
• 35 genes of the PNC 606-640 ( Figure 3) and 60 genes of PNC 682-741 ( Figure 4) are up-regulated in the malignant cancer cells and 40 genes of PNC 894-933 are up-regulated in the early recurrence cases.
• Antisense- nucleotides and siRNAs against any one of the up-regulated marker genes are useful for suppressing the expression of the up-regulated genes.
• the activity of a protein encoded by any one of the up-regulated marker genes can be inhibited by administering an antibody that binds to the protein.
• a vaccine against the protein encoded by any one of the up-regulated marker genes is useful for inducing anti tumor immunity.
• administeration of the down regulated genes or proteins encoded thereby is also effective for treating or preventing malignant pancreatic cancer or the recurrence.
• compositions for inhibiting PNC, malignant PNC, or recurrence of PNC include those suitable for oral, rectal, nasal, topical
• compositions suitable for oral administration include capsules, cachets or tablets, each containing a predetermined amount of the active ingredient.
• Formulations also include powders, granules or solutions, suspensions or emulsions.
• the active ingredient is optionally administered as a bolus electuary or paste.
• Tablets and capsules for oral administration may contain conventional excipients such as binding agents, fillers, lubricants, disintegrant or wetting agents.
• a tablet may be made by compression or molding, optionally with one or more formulational ingredients.
• Compressed tablets may be prepared by compressing in a suitable machine the active ingredients in a free-flowing form such as a powder or granules, optionally mixed with a binder, lubricant, inert diluent, lubricating, surface active or dispersing agent.
• Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent. The tablets may be coated according to methods well known in the art.
• Oral fluid preparations may be in the form of, for example, aqueous or oily suspensions, solutions, emulsions, syrups or elixirs, or may be presented as a dry product for constitution with water or other suitable vehicle before use.
• Such liquid preparations may contain conventional additives such as suspending agents, emulsifying agents, non-aqueous vehicles (which may include edible oils), or preservatives.
• the tablets may optionally be formulated so as to provide slow or controlled release of the active ingredient therein.
• a package of tablets may contain one tablet to be taken on each of the month.
• Formulations for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non- aqueous sterile suspensions which may include suspending agents and thickening agents.
• the formulations may be presented in unit dose or multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, saline, water-for-injection, immediately prior to use. Alternatively, the formulations may be presented for continuous infusion.
• Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the kind previously described.
• Formulations for rectal administration include suppositories with standard carriers such as cocoa butter or polyethylene glycol.
• Formulations for topical administration in the mouth include lozenges, which contain the active ingredient in a flavored base such as sucrose and acacia or tragacanth, and pastilles comprising the active ingredient in a base such as gelatin and glycerin or sucrose and acacia.
• the compounds of the invention may be used as a liquid spray or dispersible powder or in the form of drops. Drops may be formulated with an aqueous or non-aqueous base also comprising one or more dispersing agents, solubilizing agents or suspending agents.
• the compounds are conveniently delivered from an insufflator, nebulizer, pressurized packs or other convenient means of delivering an aerosol spray.
• Pressurized packs may comprise a suitable propellant such as dichlorodifluoromethane, trichlorofluoromethane, dichioro tefrafluoroethane, carbon dioxide or other suitable gas.
• the dosage unit may be determined by providing a valve to deliver a metered amount.
• the compounds may take the form of a dry powder composition, for example a powder mix of the compound and a suitable powder base such as lactose or starch.
• the powder composition may be presented in unit dosage form, in for example, capsules, cartridges, gelatin or blister packs from which the powder may be administered with the aid of an inhalator or insufflators.
• formulations include implantable devices and adhesive patches; which release a therapeutic agent.
• the above described formulations adapted to give sustained release of the active ingredient, may be employed.
• the pharmaceutical compositions may also contain other active ingredients such as antimicrobial agents, immunosuppressants or preservatives.
• the formulations of this invention may include other agents conventional in the art having regard to the type of formulation in question, for example, those suitable for oral administration may include flavoring agents.
• Preferred unit dosage formulations are those containing an effective dose, as recited below, or an appropriate fraction thereof, of the active ingredient.
• the compositions e.g., polypeptides and organic compounds are administered orally or via injection at a dose of from about 0.1 to about 250 mg/kg per day.
• the dose range for adult humans is generally from about 5 mg to about 17.5 g/day, preferably about 5 mg to about 10 g/day, and most preferably about 100 mg to about 3 g/day.
• Tablets or other unit dosage forms of presentation provided in discrete units may conveniently contain an amount which is effective at such dosage or as a multiple of the same, for instance, units containing about 5 mg to about 500 mg, usually from about 100 mg to about 500 mg.
• the dose employed will depend upon a number of factors, including the age and sex of the subject, the precise disorder being treated, and its severity. Also the route of administration may vary depending upon the condition and its severity.
• Pancreatic ductal adenocarcinoma that has a characteristic of highly desmoplastic stromal reaction contained a low proportion of cancer cells in the tumor mass. Furthermore, normal duct epithelial cells from which the pancreatic carcinoma originates correspond to a few percent of the pancreas tissue. Therefore, cancer cells were purified from 18 pancreatic cancers by means of laser microbeam microdissection (LMM). Gene expression profiles were examined and compared with those of normal purified pancreatic ductal epithelial cells. These cell populations had been rendered homogenous (more than 95% purified cells).
• IFITM1 interferon-induced transmembrane protein 1
• PLAU urokinase
• PSCA prostate stem cell antigen
• SI OOP SI 00 calcium binding protein P
• BIRC5 baculoviral LAP repeat-containing 5
• AXINl up-regulated l (AXUDl), deleted in liver cancer 1 (DLC1), growth arrest and DNA-damage-inducible, beta (GADD45B), p53-inducible p53DINPl (p53DINPl).
• pancreatic ductal adenocarcinoma that has a characteristic of highly desmoplastic stromal reaction contained a low proportion of cancer cells in the tumor mass.
• pancreatic ductal adenocarcinoma that has a characteristic of highly desmoplastic stromal reaction contained a low proportion of cancer cells in the tumor mass.
• the normal pancreas is mostly constituted from acinar cells and islets that accounted for more than 95% of whole pancreas, and normal duct epithelial cells from which the pancreatic carcinoma originates correspond to a few % of the pancreas.
• RNA from clinical tissue is one of the most important factors. Pancreas is known to be RNase-rich organ and degradation of RNA occurs very rapidly.
• the quality of the extracted RNA from the specimen was examined by visualization of 28S and 18S ribosomal RNAs using denaturing agarose gel electrophoresis. Following electrophoretic analysis, samples in which bands corresponding to two ribosomal RNAs were clearly observed were selected. For example, 18 cases (32%) were selected from the 56 surgically-ressected cases, i.e., many were not included in the analysis due to the poor quality of RNA.
• pancreatic cancer Over 90% of the gene expression profile of pancreatic cancer was different from previous pancreatic cancer expression profiles, because the expression data was obtained by testing highly purified cell populations obtained from patient tissues using laser dissection techniques.
• the profiles obtained and described herein represent an improvement over earlier profiles, because they were obtained by analyzing highly purified populations of cancerous cells (pancreatic ductal adenocarcinoma) and compared to a highly purified population of the most relevant normal control, i.e., normal duct epithelial cells.
• Earlier methods and profiles were hampered by a high percentage of contaminating cells, which reduced the accuracy and reliability of earlier profiles.
• This present profile is the first one of precise and genome-wide gene expression profiles in large-scale pancreatic cancer.
• Tissue obtained from diseased tissue e.g., epithelial cells from PNC
• normal tissues was evaluated to identify genes which are differently expressed or a disease state, e.g., PNC.
• the assays were carried out as follows.
• the specimens were harvested immediately after surgical resection and were embedded in TissueTek OCT medium (Sakura, Tokyo, Japan) before storage at -80°C.
• the frozen tissues were cut to 8- ⁇ m sections using a cryostat (Sakura, Tokyo, Japan) and then stained with Hematoxylin and Eosin, and check the histological state.
• Pancreatic carcinoma cells and normal pancreatic ductal epithelial cells were isolated selectively using the EZ cut system with pulsed ultraviolet narrow beam focus laser (SL Microtest GmbH, Germany) in accordance with the manufacturer's protocols. After microdissection, 7 normal cases were mixed to make a "universal control of normal pancreatic ductal epithelial cells ", that was used as a control for all 18 cancer samples.
• pancreatic cancer cells LMM was used to purify cancer cells and avoid contamination of non-cancerous cells.
• pancreatic cancer originates from pancreatic ductal cells
• pancreatic ductal epithelial cells were used as controls. The great majority of cells in pancreas are acinar cells, it was determined that the use of the entire pancreas was inappropriate for screening genes associated with pancreatic carcinogenesis.
• representative cancer cases Fig. 1A and IB
• Fig. 1C and ID normal pancreatic duct
• pancreatic cancer cells 1A and IB showed a well-differentiated type and a scirrhous type of invasive ductal adenocarcinoma, and the proportion of cancer cell was about 30% and 10%, respectively.
• LMM pancreatic cancer cells
• the proportion of acinar cells contaminated was examined in the microdissected normal pancreatic ductal epithelial cells which used as universal control (FiglC and ID).
• the signal intensity of AMY 1 A gene was examined that is known to be expressed exclusively in normal acinar cells.
• the signal intensity of whole pancreatic tissue was investigated in which >90% of the cells are acinar cells, the ratio of the average signal intensity of the pancreatic amylase gene to that of ACTB was approximately 96.7, whereas the ratio of that in microdissected normal pancreatic ductal epithelial cells in this study was calculated approximately 0.28.
• RNAs were extracted from each sample of laser-microdissected cells into 350 ⁇ l of RLT lysis buffer (QIAGEN, Hilden, Germany). The extracted RNAs were treated for 30 minutes at room temperature with 30 units of DNase I (Roche, Basel, Switzerland) in the presence of 1 unit of RNase inhibitor (TOYOBO, Osaka, Japan) to remove any contaminating genomic DNA. After inactivation at 70° C for 10 min, the RNAs were purified with an RNeasy Mini Kit (QIAGEN) according to the manufacturer's recommendations. All of the DNase I-treated RNAs were subjected to T7-based RNA amplification as described previously. Two rounds of amplification yielded 50-1 OO ⁇ g of aRNA from each sample.
• a 2.5 ⁇ g aliquot of aRNA from cancer and normal pancreatic duct epithelial cells was labeled with Cy5-dCTP or Cy3-dCTP, respectively, by a protocol described elsewhere.
• the hybridization, washing, and scanning were carried out according to the methods described previously (11).
• UniGene database (build # 131) of the National Center for Biotechnology Information (NCBI) was constructed. Briefly, the cDNAs were amplified by RT-PCR using poly(A) + RNA isolated from various human organs as templates; the lengths of the amplicons ranged from 200 to 1,100 bp that did not contain repetitive or poly(A) sequences.
• the cDNA microarray system was constructed essentially as described previously (11).
• the 12 highly up-regulated genes were selected and examined their expression levels by applying the semi-quantitative RT-PCR experiments.
• a 3- ⁇ g aliquot of aRNA from each sample was reversely-transcribed for single-stranded cDNAs using random primer (Roche) and Superscript II (Life Technologies, Inc.).
• Each cDNA mixture was diluted for subsequent PCR amplification with the same primer sets that were prepared for the target DNA or tubulin, alpha-specific reactions.
• the primer sequences are listed in Table 2. Expression of tubulin- alpha served as an internal control. PCR reactions were optimized for the number of cycles to ensure product intensity within the linear phase of amplification.
• CAAGCAGATCTACTACTCG CAGTAACCTACTTGCAGT XX
• the up- or down-regulated genes were identified common to pancreatic cancer using following criteria; 1) genes which were able to obtain expression data in more than 50% cancer cases, and 2) genes whose expression ratio was more than 5.0 in pancreatic cancer cells (defined as up-regulated genes) or genes whose expression ratio was under 0.2 (defined as down-regulated genes) in more than 50% of informative cases. Moreover, 3) the genes which were able to calculate in 33 to 50% cases and which expressed the expression ratio of more than 5.0 in all of that cases were also evaluated as up-regulated genes.
• IFITM1 interferon induced transmembrane protein 1
• PLAU urokinase
• PSCA prostate stem cell antigen
• SI OOP SI 00 calcium binding protein P
• RBMS1 RNA binding-motif single-stranded interacting protein 1
• BIRC5 baculoviral IAP repeat-containing 5
• genes such as regenerating gene type IV (REGIV), ephrin type-A receptor 4 precursor (EphA4), and vang (van gogh, Drosophila)-like 1 (VANGL1), are useful as a potential molecular target for new therapeutic agents.
• REGIV regenerating gene type IV
• EphA4 ephrin type-A receptor 4 precursor
• VANGL1 vang (van gogh, Drosophila)-like 1
• REGIV was over-expressed in all informative pancreatic cancer cases, and the overexpression was confirmed in 7 of the 12 pancreatic cancer cases by semi-quantitative RT- PCR. Since REGIV protein was thought to be a secreted protein from the amino-acid sequences and in fact its secretion was detected in the culture medium of HT29-5M12 cells (22), it is a candidate as tumor marker. EphA4 was indicated to be overexpressed in 12 of the 14 informative pancreatic cancer cases in the microarray, and confirmed in 9 of the 12 cases were examined by semi- quantitative RT-PCR.
• EphA4 is known to be a membrane receptor belonging to the ephrin family, which contains an intracellular tyrosine kinase catalytic domain (23). Involvement of EphA4 in any human cancer has not been reported. However, its nature of the cytoplasmic membrane receptor protein with possible tyrosine kinase activity as well as high level expression in cancer cells suggest that EphA4 is a candidate gene for therapeutic agents.
• VANGLl was over-expressed if all of the informative pancreatic cancer cases in the microarray data, and its high expression was also confirmed in 9 of the 12 cases by semi- quantitative RT-PCR.
• VANGLl which contained four putative fransmembrane domains, was expressed specifically in testis and ovary among 29 normal tissues examined (4). This gene was also highly and frequency transactivated in hepatocellular carcinoma. Since the enforced reduction of this gene expression in hepatocellular carcinomas induced apoptosis (4), this gene product is a good candidate for development of novel anti-cancer drugs.
• the genes that were functionally highly overexpressed in pancreatic cancer such as the above mentioned genes, those whose products are putative membranous or secreted are of interest for potential as novel anti-cancer drugs or as serological diagnostic markers for early detection.
• APP was confirmed whose over-expression in 10 of the 12 cases
• ARHGDIB was confirmed whose over-expression in 12 cases
• ATDC was confirmed whose over-expression in 10 of the 12 cases
• ATP1B3 was confirmed whose over-expression in 12 cases
• BIRC5 was confirmed whose over-expression in 12 cases
• BUB IB was confirmed whose over-expression in 12 cases
• CELSR3 was confirmed whose over-expression in 9 of the 12 cases
• CKS1 was confirmed whose over-expression in 7 of the 12 cases
• CKS2 was confirmed whose over-expression in 11 of the 12 cases
• CYP2S1 was confirmed whose over-expression in 8 of the 12 cases
• E2-EPF was confirmed whose over-expression in 8 of the 12 cases
• ELF4 was confirmed whose over-expression in 11 of the 12 cases
• ENC1 was confirmed whose over-expression in 7 of the 12 cases
• Evi-1 was confirmed whose over-expression in 11 of the 12 cases
• FOXMl was confirmed whose over-expression in 11 of the 12 cases
• GW112 was confirmed whose over-expression in 7 of the 12 cases
• GYSl was confirmed whose over-expression in 10 of the 12 cases
• HDGF was confirmed whose over-expression in 10 of the 12 cases
• HOXB7 was confirmed whose over-expression in 6 of the 12 cases
• hPAD-colonylO was confirmed whose over-expression in 6 of the 12 cases
• KNSL6 was confirmed whose over-expression in 12 cases
• KPNB2 was confirmed whose over-expression in 10 of the 12 cases
• MMP11 was confirmed whose over-expression in 10 of the 12 cases
• MYBL2 was confirmed whose over-expression in 11 of the 12 cases
• OAS1 was confirmed whose over-expression in 10 of the 12 cases
• ORP150 was confirmed whose over-expression in 8 of the 12 cases
• PCOLN3 was confirmed whose over-expression in 4 of the 12 cases
• PPM1B was confirmed whose over-expression in 3 of the 12 cases
• PRC1 was confirmed whose over-expression in 12 cases
• PSCA was confirmed whose over-expression in 6 of the 12 cases
• PYCR1 was confirmed whose over-expression in 9 of the 12 cases
• RBMS1 was confirmed whose over-expression in 12 cases
• SI OOP was confirmed whose over-expression in 10 of the 12 cases
• SFN was confirmed whose over-expression in 9 of the 12 cases
• SLC12A2 was confirmed whose over-expression in 5 of the 12 cases
• SLC2A1 was confirmed whose over-expression in 11 of the 12 cases
• SRD5A1 was confirmed whose over-expression in 8 of the 12 cases
• TCEA1 was confirmed whose over-expression in 8 of the 12 cases
• TKl was confirmed whose over-expression in 10 of the 12 cases
• UBCH10 was confirmed whose over-expression in 10 of the 12 cases
• WHSC1 was confirmed whose over-expression in 8 of the 12 cases
• FLJ10134 was confirmed whose over-expression in 8 of the 12 cases
• FLJ 10540 was confirmed whose over-expression in 11 of the 12 cases
• FLJ20225 was confirmed whose over-expression in 5 of the 12 cases
• KIAA0101 was confirmed whose over-expression in 12 cases
• KIAA1624 was confirmed whose over-expression in 9 of the 12 cases
• KIAA1808 was confirmed whose over-expression in 8 of the 12 cases
• FLJ21504 was confirmed whose over-expression in 11 of the 12 cases
• FXYD3 was confirmed whose over-expression in 9 of the 12 cases
• AI027791 was confirmed whose over-expression in 6 of the 12 cases.
• genes in pancreatic cancer cells functions of 211 genes are characterized. These included genes that have been reported to be invoved in growth suppression (24,27,28,29), such as AXINl up-regulated 1(AXUD1), Deleted in liver cancer 1 (DLC1), growth arrest and DNA-damage-inducible, beta (GADD45B), and P53- inducible p53DINPl (p53DINPl).
• AXINl up-regulated 1 AXUD1
• DLC1 Deleted in liver cancer 1
• GADD45B growth arrest and DNA-damage-inducible, beta
• p53DINPl P53- inducible p53DINPl
• the down-regulated genes are likely to have a tumor suppressive function.
• the representative tumor suppressor genes for pancreatic cancer such as SMAD4, TP53,
• INK4A, and BRCA2 were not observed in down-regulated gene list, other genes that were reported to be involved in tumor suppression or apoptosis, such as, AXINl up-regulated 1(AXUD1), deleted in liver cancer 1 (DLCl), growth arrest and DNA-damage-inducible, beta (GADD45B), p53-inducible p53DINPl ( ⁇ 53DINPl) were included in these data.
• AXUD1 a nuclear protein, is induced in response to elevation of axin that is a key mediator of the Wnt-signalling pathway and is important in axis formation in early development. Dysfunction or down-regulation of the Wnt-signaling pathway is observed in human tumors, suggesting that this gene product has a tumor suppressor function (26, 27). Hence, these data imply that down-regulation of AXUD1 might lead to down-regulation of this signaling pathway and then lead to pancreatic carcinogenesis. Deleted in liver cancer 1 (DLCl) was suggested to be a candidate tumor suppressor gene for human liver cancer, as well as for prostate, lung, colorectal, and breast cancers.
• DLCl liver cancer 1
• DLCl shares high sequence similarity with the rat pi 22 RhoGap that negatively regulates the Rho GTPases. Hence, down-regulation of DLCl is considered to result in the constitutive activation of the Rho- Rho-kinase pathway and subsequent oncogenic malignant transformation (28, 29).
• Table3 A list of up- regulated genes
• U81504 AP3B1 adaptor-related protein complex 3 beta 1 subunit amyloid beta (A4) precursor protein (protease nexin-fl, Alzheimer
• CD83 antigen activated B lymphocytes, immunoglobulin
• CYP2S1 cytochrome P540 family member predicted from ESTs
• NADH/NADPH AA921756 DIA4 diaphorase (NADH/NADPH) (cytochrome b-5 reductase)
• molybdenum cofactor biosynthesis protein A molybdenum
• PSMB3 proteasome prosome, macropain subunit
• beta type beta type
• 3 polypyrimidine tract binding protein heterogeneous nuclear
• RNASE1 ribonuclease R ⁇ ase A family, 1 (pancreatic)
• CYP2C8 polypeptide 8 cytochrome P450, subfamily IIIA (niphedipine oxidase),
• GC group supecific component
• glucose-6-phosphatase glucose-6-phosphatase
• transport glucose-6-phosphate
• Solute carrier family 25 mitochondrial carrier; citrate
• Z19002 ZNF145 promyelocytic leukemia
• zinc finger protein 42 myeloid-specific retinoic acid-

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